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@ARTICLE{Agoncillo1999,
  author = {A. V. Agoncillo and J. L. Mejino and C. Rosse},
  title = {Influence of the Digital Anatomist Foundational Model on traditional
	representations of anatomical concepts.},
  journal = {Proc AMIA Symp},
  year = {1999},
  pages = {2--6},
  abstract = {A principled and logical representation of the structure of the human
	body has led to conflicts with traditional representations of the
	same knowledge by anatomy textbooks. The examples which illustrate
	resolution of these conflicts suggest that stricter requirements
	must be met for semantic consistency, expressivity and specificity
	by knowledge sources intended to support inference than by textbooks
	and term lists. These next-generation resources should influence
	traditional concept representation, rather than be constrained by
	convention.},
  institution = {Department of Biological Structure, University of Washington, School
	of Medicine, Seattle 98195, USA.},
  keywords = {Anatomy; Anatomy, Artistic; Humans; Medical Illustration; Models,
	Anatomic; Semantics; Terminology as Topic; Textbooks as Topic},
  owner = {olivier},
  pii = {D005834},
  pmid = {10566309},
  timestamp = {2009.07.16}
}

@INPROCEEDINGS{sofa,
  author = {J\'er\'emie Allard and St\'ephane Cotin and Fran\c{c}ois Faure and
	Pierre-Jean Bensoussan and Fran\c{c}ois Poyer and Christian Duriez
	and Herv\'e Delingette and Laurent Grisoni},
  title = {{SOFA} - an Open Source Framework for Medical Simulation},
  booktitle = {Medicine Meets Virtual Reality, MMVR 15, February, 2007},
  year = {2007},
  pages = {1--6},
  address = {Long Beach, California, USA},
  note = {\url{http://www.sofa-framework.org}}
}

@ARTICLE{Brinkley1999,
  author = {Brinkley, J.F. and Wong, B.A. and Hinshaw, K.P. and Rosse, C.},
  title = {Design of an anatomy information system},
  journal = IEEE_M_CGA,
  year = {1999},
  volume = {19},
  pages = {38--48},
  number = {3},
  doi = {10.1109/38.761548},
  issn = {0272-1716},
  keywords = {data visualisation, medical computing, medical information systems,
	physiology, Digital Anatomist Project, anatomical representation
	interaction, anatomy information system design, clinical medicine,
	education, graphics, structure-based information system, visualization},
  owner = {olivier},
  timestamp = {2009.07.16}
}

@ARTICLE{Brinkley1997a,
  author = {J. F. Brinkley and C. Rosse},
  title = {The Digital Anatomist distributed framework and its applications
	to knowledge-based medical imaging.},
  journal = {J Am Med Inform Assoc},
  year = {1997},
  volume = {4},
  pages = {165--183},
  number = {3},
  abstract = {The domain of medical imaging is anatomy. Therefore, anatomic knowledge
	should be a rational basis for organizing and analyzing images. The
	goals of the Digital Anatomist Program at the University of Washington
	include the development of an anatomically based software framework
	for organizing, analyzing, visualizing and utilizing biomedical information.
	The framework is based on representations for both spatial and symbolic
	anatomic knowledge, and is being implemented in a distributed architecture
	in which multiple client programs on the Internet are used to update
	and access an expanding set of anatomical information resources.
	The development of this framework is driven by several practical
	applications, including symbolic anatomic reasoning, knowledge based
	image segmentation, anatomy information retrieval, and functional
	brain mapping. Since each of these areas involves many difficult
	image processing issues, our research strategy is an evolutionary
	one, in which applications are developed somewhat independently,
	and partial solutions are integrated in a piecemeal fashion, using
	the network as the substrate. This approach assumes that networks
	of interacting components can synergistically work together to solve
	problems larger than either could solve on its own. Each of the individual
	projects is described, along with evaluations that show that the
	individual components are solving the problems they were designed
	for, and are beginning to interact with each other in a synergistic
	manner. We argue that this synergy will increase, not only within
	our own group, but also among groups as the Internet matures, and
	that an anatomic knowledge base will be a useful means for fostering
	these interactions.},
  institution = {Department of Biological Structure, University of Washington, Seattle
	98195, USA. brinkley@u.washington.edu},
  keywords = {Anatomy; Anatomy, Artistic; Artificial Intelligence; Brain Mapping;
	Computer Communication Networks; Humans; Image Processing, Computer-Assisted;
	Information Systems; Medical Illustration; Software},
  owner = {olivier},
  pmid = {9147337},
  timestamp = {2009.07.21}
}

@INPROCEEDINGS{Charbonnier2007,
  author = {C. Charbonnier and B. Gilles and N. Magnenat-Thalmann},
  title = {A Semantic-Driven Clinical Examination Platform},
  booktitle = {In Surgetica'2007, Computer-Aided Medical Interventions: Tools and
	Applications, Chambéry, France},
  year = {2007},
  pages = {183-189},
  month = {September}
}

@INPROCEEDINGS{Cook2004,
  author = {Cook, D.L. and Mejino, J.L.V. and Rosse, C.},
  title = {The foundational model of anatomy: a template for the symbolic representation
	of multi-scale physiological functions},
  booktitle = {Proc. 26th Annual International Conference of the IEEE Engineering
	in Medicine and Biology Society IEMBS '04},
  year = {2004},
  volume = {2},
  pages = {5415--5418},
  doi = {10.1109/IEMBS.2004.1404513},
  keywords = {ontologies (artificial intelligence), physiological models, semantic
	networks, foundational model of anatomy, functional bioinformatics,
	human anatomy, knowledge representation, multiscale physiological
	functions, physiology reference ontology, semantic structure, Anatomy,
	Physiology Reference Ontology, Prot&amp, #233, g&amp, #233, -2000,
	informatics, ontology, physiology},
  owner = {olivier},
  timestamp = {2009.07.16}
}

@ARTICLE{Cook2004a,
  author = {D. L. Cook and J. L V Mejino and C. Rosse},
  title = {The foundational model of anatomy: a template for the symbolic representation
	of multi-scale physiological functions.},
  journal = {Conf Proc IEEE Eng Med Biol Soc},
  year = {2004},
  volume = {7},
  pages = {5415--5418},
  abstract = {We describe the foundational model of anatomy (FMA), reference ontology
	for the discipline of human anatomy. Using the semantic structure
	of the FMA as knowledge representation template, we propose a physiology
	reference ontology (PRO) as a corresponding ontology for "functional
	bioinformatics". We envision the PRO as a source vocabulary for building
	symbolic representations of human physiological states and actions
	that may ultimately be extensible to other species. We describe the
	evolving architecture of the PRO, in terms of simple examples based
	on the anatomical concepts encoded in the FMA.},
  doi = {10.1109/IEMBS.2004.1404513},
  institution = { Biophysics, Washington University, Seattle, WA, USA.},
  owner = {olivier},
  pmid = {17271570},
  timestamp = {2009.07.16},
  url = {http://dx.doi.org/10.1109/IEMBS.2004.1404513}
}

@ARTICLE{Cook2004b,
  author = {Daniel L Cook and Jose L V Mejino and Cornelius Rosse},
  title = {Evolution of a Foundational Model of Physiology: symbolic representation
	for functional bioinformatics.},
  journal = {Stud Health Technol Inform},
  year = {2004},
  volume = {107},
  pages = {336--340},
  number = {Pt 1},
  abstract = {We describe the need for a Foundational Model of Physiology (FMP)
	as a reference ontology for "functional bioinformatics". The FMP
	is intended to support symbolic lookup, logical inference and mathematical
	analysis by integrating descriptive, qualitative and quantitative
	functional knowledge. The FMP will serve as a symbolic representation
	of biological functions initially pertaining to human physiology
	and ultimately extensible to other species. We describe the evolving
	architecture of the FMP, which is based on the ontological principles
	of the BioD biological description language and the Foundational
	Model of Anatomy (FMA).},
  institution = {Structural Informatics Group, University of Washington, Seattle,
	WA, USA. raintown@halcyon.com},
  keywords = {Computational Biology; Humans; Models, Biological; Physiology; Vocabulary,
	Controlled},
  owner = {olivier},
  pii = {D040005412},
  pmid = {15360830},
  timestamp = {2009.07.16}
}

@ARTICLE{Detwiler2004,
  author = {Landon T Detwiler and Emily Chung and Ann Li and José L V Mejino
	and Augusto Agoncillo and James Brinkley and Cornelius Rosse and
	Linda Shapiro},
  title = {A relation-centric query engine for the Foundational Model of Anatomy.},
  journal = {Stud Health Technol Inform},
  year = {2004},
  volume = {107},
  pages = {341--345},
  number = {Pt 1},
  abstract = {The Foundational Model of Anatomy (FMA), a detailed representation
	of the structural organization of the human body, was constructed
	to support the development of software applications requiring knowledge
	of anatomy. The FMA's focus on the structural relationships between
	anatomical entities distinguishes it from other current anatomical
	knowledge sources. We developed Emily, a query engine for the FMA,
	to enable users to explore the richness and depth of these relationships.
	Preliminary analysis suggests that Emily is capable of correctly
	processing real world anatomical queries provided they have been
	translated into a constrained form suitable for processing by the
	query engine.},
  institution = {Structural Informatics Group, University of Washington, Seattle,
	WA 98195, USA.},
  keywords = {Anatomy; Artificial Intelligence; Humans; Information Storage and
	Retrieval; Models, Anatomic; User-Computer Interface; Vocabulary,
	Controlled},
  owner = {olivier},
  pii = {D040004345},
  pmid = {15360831},
  timestamp = {2009.07.16}
}

@ARTICLE{Gruber1993,
  author = {Gruber, Thomas R.},
  title = {A translation approach to portable ontology specifications},
  journal = {Knowl. Acquis.},
  year = {1993},
  volume = {5},
  pages = {199--220},
  number = {2},
  month = {June},
  address = {London, UK, UK},
  citeulike-article-id = {244074},
  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=173747},
  citeulike-linkout-1 = {http://dx.doi.org/10.1006/knac.1993.1008},
  citeulike-linkout-2 = {http://www.sciencedirect.com/science/article/B6WMS-45P67XR-D/2/b9a5cb273fc6497ae1b4fefad29b30b5},
  doi = {10.1006/knac.1993.1008},
  issn = {1042-8143},
  keywords = {ontology},
  posted-at = {2005-09-17 15:18:31},
  priority = {3},
  publisher = {Academic Press Ltd.},
  url = {http://dx.doi.org/10.1006/knac.1993.1008}
}

@INPROCEEDINGS{magnenat-thalmann09,
  author = {N. Magnenat-Thalmann and J. Schmid and H. Delingette and J.A. Iglesias
	Guitian and M. Agus},
  title = {3D Anatomical Modelling and Simulation Concepts},
  booktitle = {Eurographics 2009 Tutorial Notes},
  year = {2009},
  city = {Munich, Germany},
  mounth = {April}
}

@ARTICLE{Martin2001,
  author = {R. F. Martin and J. L. Mejino and D. M. Bowden and J. F. Brinkley
	and C. Rosse},
  title = {Foundational model of neuroanatomy: implications for the Human Brain
	Project.},
  journal = {Proc AMIA Symp},
  year = {2001},
  pages = {438--442},
  abstract = {In order to meet the need for a controlled terminology in neuroinformatics,
	we have integrated the extensive terminology of NeuroNames into the
	Foundational Model of anatomy. We illustrate the application of foundational
	principles for the establishment of an inheritance hierarchy, which
	accommodates anatomical attributes of neuroanatomical concepts and
	provides the foundation to which other information may be linked.},
  institution = {nformatics Group, Department of Biological Structure and Regional
	Primate Research Center, University of Washington, Seattle, WA 98195,
	USA.},
  keywords = {Brain; Databases as Topic; Humans; Neuroanatomy; Terminology as Topic;
	Vocabulary, Controlled},
  owner = {olivier},
  pii = {D010001583},
  pmid = {11825226},
  timestamp = {2009.07.16}
}

@ARTICLE{Martin2003,
  author = {Richard F Martin and Kurt Rickard and José L V Mejino and Augusto
	V Agoncillo and James F Brinkley and Cornelius Rosse and Structural
	Informatics Group},
  title = {The evolving neuroanatomical component of the Foundational Model
	of Anatomy.},
  journal = {AMIA Annu Symp Proc},
  year = {2003},
  pages = {927},
  abstract = {In order to meet the need for an expressive ontology in neuroinformatics,
	we have integrated the extensive terminologies of NeuroNames and
	Terminologia Anatomica into the Foundational Model of Anatomy (FMA).
	We have enhanced the FMA to accommodate information unique to neuronal
	structures, such as axonal input/output relationships.},
  institution = {.},
  keywords = {Anatomy; Humans; Neuroanatomy; Unified Medical Language System; Vocabulary,
	Controlled},
  owner = {olivier},
  pmid = {14728433},
  timestamp = {2009.07.16}
}

@ARTICLE{Mejino1999,
  author = {J. L. Mejino and C. Rosse},
  title = {Conceptualization of anatomical spatial entities in the Digital Anatomist
	Foundational Model.},
  journal = {Proc AMIA Symp},
  year = {1999},
  pages = {112--116},
  abstract = {Anatomical spatial concepts are indispensable in educational and clinical
	discourse, yet a system for representing these concepts has not been
	proposed. Guided by explicit principles and definitions of the Digital
	Anatomist Foundational Model, we developed an ontology of spaces,
	surfaces, lines and points that are associated with anatomical structures.
	Ontologies for Anatomical Structure and Anatomical Spatial Entity
	were instantiated for the thorax, abdomen, pelvis and perineum. Representing
	the concepts in--part of--hierarchies as well, provided formative
	evaluation of the classification. We invite empirical evaluation
	of the Foundational Model through its use for educational and clinical
	applications.},
  institution = {Department of Biological Structure, University of Washington School
	of Medicine, Seattle 98195, USA.},
  keywords = {Anatomy; Humans; Models, Anatomic; Terminology as Topic; Vocabulary,
	Controlled},
  owner = {olivier},
  pii = {D005410},
  pmid = {10566331},
  timestamp = {2009.07.16}
}

@ARTICLE{Mejino2003,
  author = {José V Mejino and Augusto V Agoncillo and Kurt L Rickard and Cornelius
	Rosse},
  title = {Representing complexity in part-whole relationships within the Foundational
	Model of Anatomy.},
  journal = {AMIA Annu Symp Proc},
  year = {2003},
  pages = {450--454},
  keywords = {Anatomy; Humans; Models, Anatomic; Vocabulary, Controlled},
  owner = {olivier},
  pii = {D030002797},
  pmid = {14728213},
  timestamp = {2009.07.16}
}

@ARTICLE{Michael2001,
  author = {J. Michael and J. L. Mejino and C. Rosse},
  title = {The role of definitions in biomedical concept representation.},
  journal = {Proc AMIA Symp},
  year = {2001},
  pages = {463--467},
  abstract = {The Foundational Model (FM) of anatomy, developed as an anatomical
	enhancement of UMLS, classifies anatomical entities in a structural
	context. Explicit definitions have played a critical role in the
	establishment of FM classes. Essential structural properties that
	distinguish a group of anatomical entities serve as the differentiate
	for defining classes. These, as well as other structural attributes,
	are introduced as template slots in Protégé, a frame-based knowledge
	acquisition system, and are inherited by descendants of the class.
	A set of desiderata has evolved during the instantiation of the FM
	for formulating definitions. We contend that 1. these desiderata
	generalize to non-anatomical domains and 2. satisfying them in constituent
	vocabularies of UMLS would enhance the quality of information retrievable
	through UMLS.},
  institution = {Biological Structure, University of Washington, Seattle, WA, USA.},
  keywords = {Anatomy; Artificial Intelligence; Dictionaries as Topic; Humans; Semantics;
	Terminology as Topic; Unified Medical Language System; Vocabulary,
	Controlled},
  owner = {olivier},
  pii = {D010001637},
  pmid = {11825231},
  timestamp = {2009.07.16}
}

@ARTICLE{Mork2003,
  author = {Peter Mork and James F Brinkley and Cornelius Rosse},
  title = {OQAFMA Querying agent for the Foundational Model of Anatomy: a prototype
	for providing flexible and efficient access to large semantic networks.},
  journal = {J Biomed Inform},
  year = {2003},
  volume = {36},
  pages = {501--517},
  number = {6},
  month = {Dec},
  abstract = {The development of large semantic networks, such as the UMLS, which
	are intended to support a variety of applications, requires a flexible
	and efficient query interface for the extraction of information.
	Using one of the source vocabularies of UMLS as a test bed, we have
	developed such a prototype query interface. We first identify common
	classes of queries needed by applications that access these semantic
	networks. Next, we survey StruQL, an existing query language that
	we adopted, which supports all of these classes of queries. We then
	describe the OQAFMA Querying Agent for the Foundational Model of
	Anatomy (OQAFMA), which provides an efficient implementation of a
	subset of StruQL by pre-computing a variety of indices. We describe
	how OQAFMA leverages database optimization by converting StruQL queries
	to SQL. We evaluate the flexibility and efficiency of our implementation
	using English queries written by anatomists. This evaluation verifies
	that OQAFMA provides flexible, efficient access to one such large
	semantic network, the Foundational Model of Anatomy, and suggests
	that OQAFMA could be an efficient query interface to other large
	biomedical knowledge bases, such as the Unified Medical Language
	System.},
  doi = {10.1016/j.jbi.2003.11.004},
  institution = {Department of Biological Structure, University of Washington, Seattle,
	WA 98195, USA. pmork@cs.washington.edu},
  keywords = {Abstracting and Indexing as Topic; Algorithms; Anatomy; Artificial
	Intelligence; Computational Biology; Database Management Systems;
	Databases, Factual; Information Storage and Retrieval; Linguistics;
	Models, Anatomic; National Library of Medicine (U.S.); Natural Language
	Processing; Semantics; Subject Headings; Terminology as Topic; Unified
	Medical Language System; United States; Vocabulary, Controlled},
  owner = {olivier},
  pii = {S1532046403001187},
  pmid = {14759821},
  timestamp = {2009.07.21},
  url = {http://dx.doi.org/10.1016/j.jbi.2003.11.004}
}

@ARTICLE{A-NesKryJerFau09,
  author = {Matthieu Nesme and Paul Kry and Lenka {Je\v{r}\'abkov\'a} and Fran\c{c}ois
	Faure},
  title = {Preserving Topology and Elasticity for Embedded Deformable Models},
  journal = {ACM Trans. Graph.},
  year = {2009},
  month = {aout},
  note = {Proceedings of SIGGRAPH'09}
}

@ARTICLE{Rickard2004,
  author = {Kurt L Rickard and José L V Mejino and Richard F Martin and Augusto
	V Agoncillo and Cornelius Rosse},
  title = {Problems and solutions with integrating terminologies into evolving
	knowledge bases.},
  journal = {Stud Health Technol Inform},
  year = {2004},
  volume = {107},
  pages = {420--424},
  number = {Pt 1},
  abstract = {We have merged two established anatomical terminologies with an evolving
	ontology of biological structure: the Foundational Model of Anatomy.
	We describe the problems we have encountered and the solutions we
	have developed. We believe that both the problems and solutions generalize
	to the integration of any legacy terminology with a disciplined ontology
	within the same domain.},
  institution = {Structural Informatics Group, Department of Biological Structure,
	University of Washington, Seattle, WA 98195, USA.},
  keywords = {Anatomy; Eponyms; Female; Humans; Language; Male; Neuroanatomy; Software;
	Terminology as Topic; User-Computer Interface; Vocabulary, Controlled},
  owner = {olivier},
  pii = {D040003937},
  pmid = {15360847},
  timestamp = {2009.07.16}
}

@ARTICLE{Rosse2005,
  author = {Cornelius Rosse and Anand Kumar and Jose L V Mejino and Daniel L
	Cook and Landon T Detwiler and Barry Smith},
  title = {A strategy for improving and integrating biomedical ontologies.},
  journal = {AMIA Annu Symp Proc},
  year = {2005},
  pages = {639--643},
  abstract = {The integration of biomedical terminologies is indispensable to the
	process of information integration. When terminologies are linked
	merely through the alignment of their leaf terms, however, differences
	in context and ontological structure are ignored. Making use of the
	SNAP and SPAN ontologies, we show how three reference domain ontologies
	can be integrated at a higher level, through what we shall call the
	OBR framework (for: Ontology of Biomedical Reality). OBR is designed
	to facilitate inference across the boundaries of domain ontologies
	in anatomy, physiology and pathology.},
  institution = {Structural Informatics Group, Department of Biological Structure,
	University of Washington, USA.},
  keywords = {Anatomy; Humans; Pathology; Physiology; Terminology as Topic; Vocabulary,
	Controlled},
  owner = {olivier},
  pii = {58545},
  pmid = {16779118},
  timestamp = {2009.07.16}
}

@ARTICLE{Rosse1998,
  author = {C. Rosse and J. L. Mejino and B. R. Modayur and R. Jakobovits and
	K. P. Hinshaw and J. F. Brinkley},
  title = {Motivation and organizational principles for anatomical knowledge
	representation: the digital anatomist symbolic knowledge base.},
  journal = {J Am Med Inform Assoc},
  year = {1998},
  volume = {5},
  pages = {17--40},
  number = {1},
  abstract = {OBJECTIVE: Conceptualization of the physical objects and spaces that
	constitute the human body at the macroscopic level of organization,
	specified as a machine-parseable ontology that, in its human-readable
	form, is comprehensible to both expert and novice users of anatomical
	information. DESIGN: Conceived as an anatomical enhancement of the
	UMLS Semantic Network and Metathesaurus, the anatomical ontology
	was formulated by specifying defining attributes and differentia
	for classes and subclasses of physical anatomical entities based
	on their partitive and spatial relationships. The validity of the
	classification was assessed by instantiating the ontology for the
	thorax. Several transitive relationships were used for symbolically
	modeling aspects of the physical organization of the thorax. RESULTS:
	By declaring Organ as the macroscopic organizational unit of the
	body, and defining the entities that constitute organs and higher
	level entities constituted by organs, all anatomical entities could
	be assigned to one of three top level classes (Anatomical structure,
	Anatomical spatial entity and Body substance). The ontology accommodates
	both the systemic and regional (topographical) views of anatomy,
	as well as diverse clinical naming conventions of anatomical entities.
	CONCLUSIONS: The ontology formulated for the thorax is extendible
	to microscopic and cellular levels, as well as to other body parts,
	in that its classes subsume essentially all anatomical entities that
	constitute the body. Explicit definitions of these entities and their
	relationships provide the first requirement for standards in anatomical
	concept representation. Conceived from an anatomical viewpoint, the
	ontology can be generalized and mapped to other biomedical domains
	and problem solving tasks that require anatomical knowledge.},
  institution = {Department of Biological Structure, University of Washington, Seattle
	98195, USA. rosse@u.washington.edu},
  keywords = {Anatomy; Artificial Intelligence; Humans; Semantics; Terminology as
	Topic; Thorax; Unified Medical Language System; Vocabulary, Controlled},
  owner = {olivier},
  pmid = {9452983},
  timestamp = {2009.07.16}
}

@ARTICLE{Rosse2003,
  author = {Cornelius Rosse and José L V Mejino},
  title = {A reference ontology for biomedical informatics: the Foundational
	Model of Anatomy.},
  journal = {J Biomed Inform},
  year = {2003},
  volume = {36},
  pages = {478--500},
  number = {6},
  month = {Dec},
  abstract = {The Foundational Model of Anatomy (FMA), initially developed as an
	enhancement of the anatomical content of UMLS, is a domain ontology
	of the concepts and relationships that pertain to the structural
	organization of the human body. It encompasses the material objects
	from the molecular to the macroscopic levels that constitute the
	body and associates with them non-material entities (spaces, surfaces,
	lines, and points) required for describing structural relationships.
	The disciplined modeling approach employed for the development of
	the FMA relies on a set of declared principles, high level schemes,
	Aristotelian definitions and a frame-based authoring environment.
	We propose the FMA as a reference ontology in biomedical informatics
	for correlating different views of anatomy, aligning existing and
	emerging ontologies in bioinformatics ontologies and providing a
	structure-based template for representing biological functions.},
  doi = {10.1016/j.jbi.2003.11.007},
  institution = { Biomedical Informatics, Structural Informatics Group, University
	of Washington, Seattle, WA 98195, USA. rosse@u.washington.edu},
  keywords = {Abstracting and Indexing as Topic; Algorithms; Anatomy; Artificial
	Intelligence; Computational Biology; Database Management Systems;
	Databases, Factual; Humans; Information Storage and Retrieval; Linguistics;
	Models, Anatomic; National Library of Medicine (U.S.); Natural Language
	Processing; Semantics; Subject Headings; Terminology as Topic; Unified
	Medical Language System; United States; Vocabulary, Controlled},
  owner = {olivier},
  pii = {S1532046403001278},
  pmid = {14759820},
  timestamp = {2009.07.16},
  url = {http://dx.doi.org/10.1016/j.jbi.2003.11.007}
}

@ARTICLE{Rubin2006,
  author = {Daniel L Rubin and David Grossman and Maxwell Neal and Daniel L Cook
	and James B Bassingthwaighte and Mark A Musen},
  title = {Ontology-based representation of simulation models of physiology.},
  journal = {AMIA Annu Symp Proc},
  year = {2006},
  pages = {664--668},
  abstract = {Dynamic simulation models of physiology are often represented as a
	set of mathematical equations. Such models are very useful for studying
	and understanding the dynamic behavior of physiological variables.
	However, the sheer number of equations and variables can make these
	models unwieldy, difficult to under-stand, and challenging to maintain.
	We describe a symbolic, ontologically-guided methodology for representing
	a physiological model of the circulation. We created an ontology
	describing the types of equations in the model as well as the anatomic
	components and how they are connected to form a circulatory loop.
	The ontology provided an explicit representation of the model, both
	its mathematical and anatomic content, abstracting and hiding much
	of the mathematical complexity. The ontology also provided a framework
	to construct a graphical representation of the model, providing a
	simpler visualization than the large set of mathematical equations.
	Our approach may help model builders to maintain, debug, and extend
	simulation models.},
  institution = {Stanford Medical Informatics, Stanford University School of Medicine,
	Stanford, CA, USA.},
  keywords = {Blood Circulation; Cardiovascular Physiological Phenomena; Cardiovascular
	System; Computer Simulation; Humans; Models, Cardiovascular; Software;
	Vocabulary, Controlled},
  owner = {olivier},
  pii = {85984},
  pmid = {17238424},
  timestamp = {2009.07.19}
}

@ARTICLE{Smith2005a,
  author = {Barry Smith and Werner Ceusters and Bert Klagges and Jacob Köhler
	and Anand Kumar and Jane Lomax and Chris Mungall and Fabian Neuhaus
	and Alan L Rector and Cornelius Rosse},
  title = {Relations in biomedical ontologies.},
  journal = {Genome Biol},
  year = {2005},
  volume = {6},
  pages = {R46},
  number = {5},
  abstract = {To enhance the treatment of relations in biomedical ontologies we
	advance a methodology for providing consistent and unambiguous formal
	definitions of the relational expressions used in such ontologies
	in a way designed to assist developers and users in avoiding errors
	in coding and annotation. The resulting Relation Ontology can promote
	interoperability of ontologies and support new types of automated
	reasoning about the spatial and temporal dimensions of biological
	and medical phenomena.},
  doi = {10.1186/gb-2005-6-5-r46},
  institution = {on Science, Saarland University, D-66041 Saarbrücken, Germany. phismith@buffalo.edu},
  keywords = {Biomedical Research; Computational Biology; Terminology as Topic;
	Vocabulary, Controlled},
  owner = {olivier},
  pii = {gb-2005-6-5-r46},
  pmid = {15892874},
  timestamp = {2009.07.23},
  url = {http://dx.doi.org/10.1186/gb-2005-6-5-r46}
}

@ARTICLE{Trelease2002,
  author = {Robert B Trelease},
  title = {Anatomical informatics: Millennial perspectives on a newer frontier.},
  journal = {Anat Rec},
  year = {2002},
  volume = {269},
  pages = {224--235},
  number = {5},
  month = {Oct},
  abstract = {One of the most ancient of sciences, anatomy has evolved over many
	centuries. Its methods have progressively encompassed dissection
	instruments, manual illustration, stains, microscopes, cameras and
	photography, and digital imaging systems. Like many other more modern
	scientific disciplines in the late 20th century, anatomy has also
	benefited from the revolutionary development of digital computers
	and their automated information management and analytical capabilities.
	By using newer methods of computer and information sciences, anatomists
	have made outstanding contributions to science, medicine, and education.
	In that regard, there is a strong rationale for recognizing anatomical
	informatics as a proper subdiscipline of anatomy. A high-level survey
	of the field reveals important anatomical applications of computer
	sciences methods in imaging, image processing and visualization,
	virtual reality, modeling and simulation, structural database processing,
	networking, and artificial intelligence. Within this framework, computational
	anatomy is a developing field focusing on data-driven mathematical
	models of bodily structures. Mastering such computer sciences and
	informatics methods is crucial for new anatomists, who will shape
	the future in research, clinical knowledge, and teaching.},
  doi = {10.1002/ar.10177},
  institution = {Division of Integrative Anatomy, Department of Pathology and Laboratory
	Medicine, UCLA School of Medicine, Los Angeles, CA 90095, USA. trelease@ucla.edu},
  keywords = {Anatomy; Computer-Assisted Instruction; Databases, Factual; Humans;
	Image Processing, Computer-Assisted; Imaging, Three-Dimensional;
	Internet; Medical Informatics Applications},
  owner = {olivier},
  pmid = {12379939},
  timestamp = {2009.07.21},
  url = {http://dx.doi.org/10.1002/ar.10177}
}

@ARTICLE{A-WonRosBri99,
  author = {B.A. Wong and C. Rosse and J.F. Brinkley},
  title = {Semi-automatic Scene Generation using the Digital Anatomist Foundational
	Model},
  journal = {J. Am. Med. Assoc.},
  year = {1999},
  volume = {AMIA '99 Symp.},
  pages = {637-641},
  note = {Suppl.}
}

@ARTICLE{Zhang2006a,
  author = {Songmao Zhang and Olivier Bodenreider},
  title = {Law and order: assessing and enforcing compliance with ontological
	modeling principles in the Foundational Model of Anatomy.},
  journal = {Comput Biol Med},
  year = {2006},
  volume = {36},
  pages = {674--693},
  number = {7-8},
  abstract = {The objective of this study is to provide an operational definition
	of principles with which well-formed ontologies should comply. We
	define 15 such principles, related to classification (e.g., no hierarchical
	cycles are allowed; concepts have a reasonable number of children),
	incompatible relationships (e.g., two concepts cannot stand both
	in a taxonomic and partitive relation), dependence among concepts,
	and the co-dependence of equivalent sets of relations. Implicit relations--embedded
	in concept names or inferred from a combination of explicit relations--are
	used in this process in addition to the relations explicitly represented.
	As a case study, we investigate the degree to which the Foundational
	Model of Anatomy (FMA)--a large ontology of anatomy--complies with
	these 15 principles. The FMA succeeds in complying with all the principles:
	totally with one and mostly with the others. Reasons for non-compliance
	are analyzed and suggestions are made for implementing effective
	enforcement mechanisms in ontology development environments. The
	limitations of this study are also discussed.},
  doi = {10.1016/j.compbiomed.2005.04.007},
  institution = {U.S. National Library of Medicine, National Institutes of Health,
	Bethesda, MD, USA. smzhang@math.ac.cn},
  keywords = {Anatomy; Classification; Humans; Medical Informatics; Models, Anatomic},
  owner = {olivier},
  pii = {S0010-4825(05)00072-7},
  pmid = {16144698},
  timestamp = {2009.07.21},
  url = {http://dx.doi.org/10.1016/j.compbiomed.2005.04.007}
}

@article{Attene07,
title={{Semantic annotation of 3d surface meshes based on feature characterization}},
author={Attene, M. and Robbiano, F. and Spagnuolo, M. and Falcidieno, B.},
journal={Lecture Notes in Computer Science},
volume={4816},
pages={126},
year={2007},
publisher={Springer}
}


@article{DeFloriani07,
title={{A Semantic Web Environment for Digital Shapes Understanding}},
author={De Floriani, L. and Hui, L. and Papaleo, L. and Huang, M.  and  Hendler, J.}
journal={Lecture Notes in Computer Science},
volume={4816},
pages={226-239},
year={2007},
publisher={Springer}
}

@ARTICLE{Smith2007,
  author = {Barry Smith and Michael Ashburner and Cornelius Rosse and Jonathan
	Bard and William Bug and Werner Ceusters and Louis J Goldberg and
	Karen Eilbeck and Amelia Ireland and Christopher J Mungall and O.
	B. I. Consortium and Neocles Leontis and Philippe Rocca-Serra and
	Alan Ruttenberg and Susanna-Assunta Sansone and Richard H Scheuermann
	and Nigam Shah and Patricia L Whetzel and Suzanna Lewis},
  title = {The OBO Foundry: coordinated evolution of ontologies to support biomedical
	data integration.},
  journal = {Nat Biotechnol},
  year = {2007},
  volume = {25},
  pages = {1251--1255},
  number = {11},
  month = {Nov},
  abstract = {The value of any kind of data is greatly enhanced when it exists in
	a form that allows it to be integrated with other data. One approach
	to integration is through the annotation of multiple bodies of data
	using common controlled vocabularies or 'ontologies'. Unfortunately,
	the very success of this approach has led to a proliferation of ontologies,
	which itself creates obstacles to integration. The Open Biomedical
	Ontologies (OBO) consortium is pursuing a strategy to overcome this
	problem. Existing OBO ontologies, including the Gene Ontology, are
	undergoing coordinated reform, and new ontologies are being created
	on the basis of an evolving set of shared principles governing ontology
	development. The result is an expanding family of ontologies designed
	to be interoperable and logically well formed and to incorporate
	accurate representations of biological reality. We describe this
	OBO Foundry initiative and provide guidelines for those who might
	wish to become involved.},
  doi = {10.1038/nbt1346},
  institution = {w York State Center of Excellence in Bioinformatics and Life Sciences,
	University at Buffalo, Buffalo, New York 14203, USA. phismith@buffalo.edu},
  keywords = {Humans; Information Storage and Retrieval; Nervous System; Nervous
	System Physiological Phenomena; Terminology as Topic; Vocabulary,
	Controlled},
  owner = {olivier},
  pii = {nbt1346},
  pmid = {17989687},
  timestamp = {2009.09.15},
  url = {http://dx.doi.org/10.1038/nbt1346}
}



@MISC{3dha,
  note = {Webpage 3D Anatomical Human project \url{http://3dah.miralab.unige.ch},
	Accessed March 2008.}
}

@MISC{blender,
  note = {\url{http://www.blender.org}}
}

@MISC{focus3D,
  note = {\url{http://www.focusedk3d.eu}}
}

